The report was generated using the JSEQ_scRNAseq single-cell analysis pipeline. For more information, please visit: https://github.com/jkubis96/JSEQ_scRNAseq


1 Analysis Configuration Parameters

Parameter Value
mt_per 25
scale_factor 1e+06
n_features 2000
c_res 0.5
heterogeneity deg
mt_cssg FALSE
m_val 0.05
top_m 50
max_genes 1000
max_combine 1000
loss_val 0.05
s_factor 0.8
p_bin 0.05
drop TRUE
min_c 10

The parameters above were used during the current analysis.
If you need to apply different analysis conditions, modify the parameters in the configuration file.

Parameters description:

  • mt_per
    Maximum percentage of mitochondrial genes per cell.
    Default: 25%
  • down
    Lower threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • up
    Upper threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • scale_factor
    Scale factor used for data normalization.
  • n_features
    Number of variable features to detect for clustering.
  • c_res
    Clustering resolution — higher values produce more clusters.
  • heterogeneity
    Method for estimating cluster heterogeneity.
    Options: var (within-cluster variance), deg (deregulated gene profiles).
    Default: deg
  • mt_cssg
    Whether to include mitochondrial genes when creating subclasses and subtypes.
    Options: TRUE, FALSE.
    Default: FALSE
  • m_val
    Maximum p-value threshold for marker detection in advanced subtype analyses.
    Default: 0.05
  • top_m
    Maximum number of top markers used for naming clusters based on effect size metrics.
    Default: 50
  • max_genes
    Maximum number of input genes considered in cluster heterogeneity discovery.
    Default: 1000
  • max_combine
    Maximum number of initial combinations for each iteration during heterogeneity discovery.
    Default: 1000
  • loss_val
    Assigned value for potentially unclassified cells within a cluster.
  • s_factor
    Maximum split factor for gene occurrence in heterogeneity discovery (0.2–1).
    Default: 0.8
  • p_bin
    Minimum cell proportion required for population presence based on binomial test p-value.
    Default: 0.05
  • min_c
    Minimum cell proportion required for population presence as defined by the user (independent of binomial test).
    Default: 10
  • drop
    Boolean indicating whether to drop non-significant subtypes based on p_bin and min_c.
    Default: TRUE

The configuration file is available in the directory:
JSEQ_scRNAseq/requirements_file/config_file.conf

Additional configuration files for other analysis steps can also be found in:
JSEQ_scRNAseq/requirements_file

For more information, please visit:
https://github.com/jkubis96/JSEQ_scRNAseq



2 Cell content analysis

2.1 Read distribution across genomic features

2.2 Count (UMI) per barcode (cell)

2.3 Cell barcode knee plot

The above graph illustrates general trends and quality metrics at the initial stage of single-cell analysis; however, it does not represent the final number of detected cells.

2.4 Ratio of number of genes to counts

2.5 Number of genes and counts per cell

2.6 Percentage of ribosomal and mitochondrial genes [%]



3 Quality control of cell content

3.1 Genes per cell content & thresholds

3.2 Genes upper & lower thresholds per cell

3.3 Number of cells across different stages of analysis



4 Gene expression analysis across cells

4.1 Top highly variable genes in the dataset



5 Princilpe component selection

5.1 ElbowPlot - principal components cutoff

5.2 JackStrawPlot - PC significance



6 Cells clustering

6.1 UMAP clusters



7 Subclasses identification based on marker genes

7.1 PCA cisualization of subclasses

7.2 UMAP visualization of subclasses

7.3 Subclasses - cell composition


7.4 Subclasses markers - top 25


Top 25 merkers
genes pct_occurrence esm avg_logFC p_val cluster p_adj_bf p_adj_bh subclass
MT-RNR2 0.9480519 0.2943721 0.1088171 0.0000000 0 0.0000000 0.0000000 TEG ZFPM2 ENSG00000233755
PPFIBP2 0.0519481 0.1604065 1.2272448 0.0230524 0 0.2766286 0.1383143 TEG ZFPM2 ENSG00000233755
ENSG00000233755 0.0930736 0.1448644 0.7404038 0.0463976 0 0.5567715 0.1391929 TEG ZFPM2 ENSG00000233755
MT-ND4L 0.4004329 0.0325188 0.0568023 0.0359697 0 0.4316363 0.1391929 TEG ZFPM2 ENSG00000233755
PNISR 0.5523466 1.1303595 2.3654247 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRSF11 0.4873646 1.1180884 2.6664348 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
RBM25 0.5306859 1.0064723 2.1314647 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
ARGLU1 0.4584838 0.9865719 2.4018108 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SETD5 0.3790614 0.9864712 2.9526072 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
LUC7L3 0.5956679 0.9764462 1.7980896 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPA2B1 0.4945848 0.9211209 2.0289638 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRRM2 0.3285199 0.8697239 2.8167677 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPR 0.4620939 0.8639703 2.0043969 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PRRC2C 0.5126354 0.8639157 1.8199530 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPD 0.4187726 0.8598310 2.1713607 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
BPTF 0.3718412 0.8493818 2.4042235 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
TXNIP 0.4981949 0.8373820 1.7793625 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
ZRANB2 0.3285199 0.8223846 2.5957504 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
DDX5 0.4296029 0.8172000 1.9875079 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
TIA1 0.2418773 0.8120068 3.4977910 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HSP90AB1 0.6534296 0.8035374 1.2849250 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPDL 0.4981949 0.7992691 1.6882866 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
NKTR 0.2707581 0.7815232 2.8901096 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PAFAH1B1 0.3971119 0.7780055 2.0036973 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SON 0.3790614 0.7681067 2.0704723 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PNN 0.3357401 0.7631730 2.2836210 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
DDX17 0.4332130 0.7570656 1.7915320 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRRM1 0.4332130 0.7509675 1.7794081 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
CEP95 0.2093863 0.7463068 3.5299231 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SUZ12 0.8571429 0.6521914 0.5823289 0.0000000 2 0.0000000 0.0000000 TEG ZFPM2 KCNG4
CHST11 0.4081633 0.6284434 1.2635037 0.0000000 2 0.0000007 0.0000003 TEG ZFPM2 KCNG4
KCNG4 0.1530612 0.5739845 2.1895728 0.0000002 2 0.0000273 0.0000091 TEG ZFPM2 KCNG4
DOCK4 0.1122449 0.4974462 2.2032658 0.0000184 2 0.0021525 0.0005381 TEG ZFPM2 KCNG4
ANKRD30BL 0.0816327 0.4840782 2.5935197 0.0000234 2 0.0027389 0.0005478 TEG ZFPM2 KCNG4
SLC12A2 0.2244898 0.4783686 1.3935272 0.0000329 2 0.0038487 0.0006414 TEG ZFPM2 KCNG4
IL1F10 0.0612245 0.4505006 2.8776636 0.0000454 2 0.0053174 0.0007596 TEG ZFPM2 KCNG4
ENSG00000254840 0.2244898 0.4355335 1.2642208 0.0001337 2 0.0156384 0.0019548 TEG ZFPM2 KCNG4
LINC01716 0.0510204 0.3978794 2.7295115 0.0005508 2 0.0644419 0.0053702 TEG ZFPM2 KCNG4
LINC01681 0.0816327 0.3918819 2.1046915 0.0003642 2 0.0426056 0.0042606 TEG ZFPM2 KCNG4
RFX2 0.3673469 0.3751707 0.7883006 0.0003328 2 0.0389390 0.0042606 TEG ZFPM2 KCNG4
SMYD3.var1 0.0612245 0.3474395 2.0923919 0.0050499 2 0.5908436 0.0365260 TEG ZFPM2 KCNG4
APOH 0.1632653 0.3458943 1.2131972 0.0029723 2 0.3477640 0.0248403 TEG ZFPM2 KCNG4
NOTCH2 0.0510204 0.3197307 2.1900200 0.0048527 2 0.5677616 0.0365260 TEG ZFPM2 KCNG4
MAP3K10 0.0714286 0.2993358 1.6681662 0.0130372 2 1.0000000 0.0847419 TEG ZFPM2 KCNG4
UNC13C 0.0510204 0.2933437 2.0661576 0.0053072 2 0.6209426 0.0365260 TEG ZFPM2 KCNG4
LINC00486 0.2040816 0.2705040 0.8274494 0.0146749 2 1.0000000 0.0903667 TEG ZFPM2 KCNG4
NMNAT2 0.0612245 0.2680150 1.6439134 0.0230783 2 1.0000000 0.1285791 TEG ZFPM2 KCNG4
IQSEC1 0.0510204 0.2624504 1.7138774 0.0492255 2 1.0000000 0.2206001 TEG ZFPM2 KCNG4
ENSG00000250961 0.0816327 0.2487368 1.3225915 0.0248751 2 1.0000000 0.1293415 TEG ZFPM2 KCNG4
ENSG00000233755 0.1326531 0.2482931 1.0022172 0.0254261 2 1.0000000 0.1293415 TEG ZFPM2 KCNG4
ZFPM2 0.2653061 0.2434642 0.6203788 0.0228340 2 1.0000000 0.1285791 TEG ZFPM2 KCNG4
TRIM71 0.0612245 0.2357298 1.4377222 0.0485614 2 1.0000000 0.2206001 TEG ZFPM2 KCNG4
MT-ND4 0.5918367 0.2074306 0.2697502 0.0004226 2 0.0494445 0.0044950 TEG ZFPM2 KCNG4
MT-RNR2 0.9591837 0.1917874 0.0753420 0.0021947 2 0.2567854 0.0197527 TEG ZFPM2 KCNG4
HS6ST3 0.5614035 2.9228573 4.6567511 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
DOCK9 0.6666667 2.6089908 3.6496134 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000254840 0.7192982 2.4793407 3.3678033 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
CYRIB 0.5087719 2.2168804 3.8573725 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
RFX2 0.8947368 2.1067320 2.3835340 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ANKFN1.var1 0.4912281 2.0383039 3.6595689 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC00486 0.6666667 2.0056607 2.9108364 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
APOH 0.5087719 1.8847868 3.2672138 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ZFPM2 0.7719298 1.8332059 2.4084283 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
CHST11 0.7894737 1.8286630 2.3561399 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000240963 0.2631579 1.8127933 4.8245490 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
UBE2E2.var1 0.5789474 1.6353313 2.6578025 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
PHF20 0.3333333 1.6347562 3.6764777 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
TYW1B.var1 0.2105263 1.5759874 4.9236294 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
WDR88 0.2807018 1.5756224 4.0407607 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
BACH2 0.3508772 1.5001488 3.3491957 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC00536.var1 0.1929825 1.4237528 4.6923754 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
SLC12A2 0.4736842 1.4225603 2.6176585 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000279465 0.2982456 1.3899192 3.3768871 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
RIOX2 0.1578947 1.3752147 5.0779323 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000288011 0.2280702 1.3710866 4.0603534 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC02814 0.2280702 1.3645709 3.9046559 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000226197 0.1754386 1.3451350 4.6182786 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000246225 0.2280702 1.3323424 3.7632144 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
DUXAP10 0.1929825 1.3200506 4.0979211 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9


7.5 Heatmap of cell subclasses - log(CPM + 1)

7.6 Heatmap of cell subclasses - scale(log(CPM + 1))




8 Subtypes identification based on CSSG genes

8.1 UMAP visualization


8.2 Subtypes - cell composition


8.3 Subtypes markers - top 25


Top 25 markers
genes pct_occurrence esm avg_logFC p_val subtype p_adj_bf p_adj_bh cluster
PPFIBP2 1.0000000 5.8573977 5.0510830 0.0000000 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0000000 0.0000000 0
ENSG00000233755 1.0000000 5.0523329 4.4536751 0.0000000 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0000000 0.0000000 0
MPP7.var1 0.2500000 0.8360283 2.3210410 0.0006096 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0347495 0.0173747 0
GNAI1 0.1500000 0.8266246 2.8958131 0.0016711 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0952512 0.0317504 0
LMBRD1 0.1500000 0.6580889 2.2642754 0.0260400 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
KCNG4 0.1627907 0.6379853 2.3419154 0.0001590 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0027023 0.0009008 0
ENSG00000243199 0.2000000 0.5741576 1.7923164 0.0259656 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
KCNG4 0.1500000 0.5433497 2.0647710 0.0239265 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
PPM1H.var1 0.1162791 0.4420487 1.8733241 0.0187015 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.3179248 0.0794812 0
MPP7.var1 0.1395349 0.4075389 1.5667299 0.0264723 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.4500292 0.0900058 0
MT-RNR2 0.9534884 0.3529472 0.1439651 0.0000058 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0000986 0.0000493 0
RBM25 0.5306859 1.1088582 3.1600885 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
SRSF11 0.4873646 1.1065830 3.9575185 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HSP90AB1 0.6534296 1.0351984 1.8452727 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
LUC7L3 0.5956679 1.0068706 2.0800146 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPA2B1 0.4945848 0.9703982 2.7260866 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
PNISR 0.5523466 0.9380181 2.0984619 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
PRRC2C 0.5126354 0.8955268 2.2089133 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL23 0.4981949 0.8816947 2.2293477 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
TXNIP 0.4981949 0.8722371 2.1973544 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
MALAT1 1.0000000 0.8630070 0.0856148 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPR 0.4620939 0.8515161 2.3679298 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
SETD5 0.3790614 0.8372310 3.2396141 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
YBX1 0.6425993 0.8210745 1.3645736 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000036 0.0000001 1
SON 0.3790614 0.8167009 3.0301491 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL24 0.4584838 0.7993041 2.1432523 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPDL 0.4981949 0.7871019 1.8504950 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ARGLU1 0.4584838 0.7848145 2.0683080 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPS8 0.5956679 0.7726763 1.3880136 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000045 0.0000001 1
NCL 0.4332130 0.7707967 2.1775199 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
DDX5 0.4296029 0.7660591 2.1735043 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
FNBP1L 0.3790614 0.7637418 2.6240189 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ZRANB2 0.3285199 0.7622448 3.3410808 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL14 0.4801444 0.7586489 1.8283251 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ZNF638 0.3249097 0.7551620 3.3297034 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
DDX17 0.4332130 0.7538637 2.0868450 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
CHST11 1.0000000 1.7715617 1.8814283 0.0000000 TEG ZFPM2 KCNG4 - CHST11 0.0000000 0.0000000 2
RFX2 1.0000000 1.6204503 1.7126613 0.0000000 TEG ZFPM2 KCNG4 - RFX2 0.0000000 0.0000000 2
KCNG4 0.2400000 0.9986802 2.8422320 0.0000034 TEG ZFPM2 KCNG4 - RFX2 0.0002457 0.0001229 2
OLFM2 0.1200000 0.9875768 3.9219536 0.0000168 TEG ZFPM2 KCNG4 - CHST11 0.0012409 0.0005895 2
PRDX3 0.1200000 0.9522948 3.7088663 0.0000726 TEG ZFPM2 KCNG4 - CHST11 0.0053698 0.0011388 2
ENSG00000287277 0.1200000 0.9056296 3.6055735 0.0000769 TEG ZFPM2 KCNG4 - CHST11 0.0056940 0.0011388 2
APBB2.var1 0.1200000 0.7915785 3.0190525 0.0026826 TEG ZFPM2 KCNG4 - CHST11 0.1985142 0.0183900 2
FAM217B 0.1200000 0.7760776 3.0604234 0.0014143 TEG ZFPM2 KCNG4 - CHST11 0.1046580 0.0133561 2
PSMC4 0.1200000 0.7677183 3.0421751 0.0014439 TEG ZFPM2 KCNG4 - CHST11 0.1068484 0.0133561 2
PDE1C.var2 0.1600000 0.7387529 2.6052553 0.0009081 TEG ZFPM2 KCNG4 - RFX2 0.0662914 0.0132583 2
CFAP251 0.1200000 0.7038845 2.8365546 0.0027336 TEG ZFPM2 KCNG4 - CHST11 0.2022896 0.0183900 2
NOTCH2 0.1200000 0.6999009 2.8973582 0.0015362 TEG ZFPM2 KCNG4 - RFX2 0.1121391 0.0186898 2
LINC01681 0.1600000 0.6565175 2.3951640 0.0019482 TEG ZFPM2 KCNG4 - CHST11 0.1441643 0.0160183 2
FGF14.var1 0.1200000 0.6336429 2.6228657 0.0050368 TEG ZFPM2 KCNG4 - CHST11 0.3727254 0.0310605 2
SUZ12 0.9200000 0.6154919 0.4631502 0.0000239 TEG ZFPM2 KCNG4 - CHST11 0.0017685 0.0005895 2
ACACA 0.1200000 0.6145135 2.5288983 0.0081171 TEG ZFPM2 KCNG4 - CHST11 0.6006618 0.0462048 2
RNF11 0.1200000 0.5992690 2.4460914 0.0122911 TEG ZFPM2 KCNG4 - CHST11 0.9095444 0.0649675 2
CCDC59 0.1600000 0.5482939 1.8942742 0.0273406 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.2851236 2
ENSG00000223720 0.1200000 0.5288439 2.1660477 0.0310382 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.1351075 2
SLC12A2 0.3200000 0.5031046 1.2091560 0.0176591 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.0816736 2
MT-RNR2 1.0000000 0.5014454 0.2040283 0.0004337 TEG ZFPM2 KCNG4 - CHST11 0.0320962 0.0053494 2
ENSG00000288011 0.1200000 0.4605178 1.9943422 0.0353197 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.1452034 2
LINC01681 0.1200000 0.4547029 1.9804388 0.0337078 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.3075841 2
ENSG00000250961 0.1200000 0.4435947 1.9158981 0.0444826 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.3608032 2
SUZ12 0.8400000 0.4059101 0.3302442 0.0005535 TEG ZFPM2 KCNG4 - RFX2 0.0404030 0.0101007 2
HS6ST3 0.6400000 2.8083795 4.4863348 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
DOCK9 0.7600000 2.5716783 3.3446878 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000254840 0.7600000 2.1490569 2.8716808 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
RFX2 1.0000000 2.1154226 2.0394933 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
LINC00486 0.6800000 1.7796119 2.5842787 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
CYRIB 0.5000000 1.7586755 3.3359301 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ANKFN1.var1 0.4600000 1.6091175 3.2236735 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ZFPM2 0.7800000 1.6022997 2.0303586 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
APOH 0.5200000 1.5681949 2.7962511 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
UBE2E2.var1 0.6200000 1.5560982 2.4346618 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000240963 0.3000000 1.4812872 4.1026400 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000226197 0.2000000 1.3261443 5.2869060 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000279465 0.3400000 1.3202787 3.2119882 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
WDR88 0.2800000 1.2716937 3.5990320 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
PHF20 0.3600000 1.2613889 2.9082193 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
CHST11 0.7600000 1.2586773 1.5967919 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
SUZ12 0.9800000 1.2239267 0.7797739 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000223393 0.6600000 1.2196831 1.7456567 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000288011 0.2400000 1.1912343 3.8843482 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
RIOX2 0.1600000 1.1543542 5.0747074 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
TYW1B.var1 0.2000000 1.1370017 4.0775352 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000246225 0.2600000 1.1215573 3.2035191 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
LINC02814 0.2600000 1.1205603 3.2522165 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
TRIM71 0.2200000 1.1192474 3.7124839 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
MAP1LC3BP1 0.1800000 1.1115284 4.2686929 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3


8.4 Heatmap of cell subtypes - log(CPM + 1)

8.5 Heatmap of cell subtypes - scale(log(CPM + 1))




9 Disclaimer

The analysis was performed through the non-profit and open-source pipeline JSEQ_scRNAseq. Remember, in silico analysis must be validated in vitro or in vivo. For more information, visit GitHub or contact us. JSEQ_scRNAseq was created at the Institute of Bioorganic Chemistry, Polish Academy of Sciences.